The real power is and have always been with the council of ministers who is appointed by the member governments, and in practice only responsible to the member parliaments and not the EU parliament, who barely have authority to overrule the larger and more permanent commission, let alone propose any legislation.
Don't get me wrong I am pro EU but the current structure is pretty strange and mostly dysfunctional in trying to spread the pain evenly and prone to being dominated by large corporate interest groups.